The emergence of functional genomics has led to a growing need for analyzing molecular variants and post-translational modifications of proteins that often determine the biological results of changes at the genomic level. The proposed work is aimed at utilizing aptamers, oligonucleotide ligands for specific target molecules, to distinguish between these molecular variants. To accomplish this, affinity probe capillary electrophoresis (APCE) will be applied as a rapid method to detect fluorescently labeled aptamers that are bound to their targets. In particular, the ability of aptamers for vascular endothelial growth factor (VEGF), a protein implicated in tumor growth, to bind selected peptide domains of the VEGF protein will be investigated. After establishing reliable APCE methods for a selected peptide domain, specific modified peptides that incorporate phosphoserine and/or phosphothreonine will be investigated as models of typical post-translational modifications. Capillary electrophoresis aptamer selection will further identify oligonucleotide sequences that preferentially bind specific peptides. These studies will lead to the development of aptamer arrays for individual molecules, each targeting a particular domain or functional modification of the protein. Such panels would be novel molecular tools for rapid and simple monitoring of disease-linked functional changes in protein molecules with potential applications in drug screening and disease diagnosis. This work will lead to the development of aptamers that target specific domains or functional modifications of target proteins. Such aptamers could be used for signaling the presence of proteins associated with particular disease states, or potentially as pharmaceutical agents that can block or modify the action of these proteins.